Mitotree is Born

Mitotree is born and I can hardly contain my excitement.

The Million Mito R&D team members, along with many others at FamilyTreeDNA, are proud to introduce the new Mitotree and mtDNA Discover, which were brought to life thanks to one pivotal entrepreneurial figure, Bennett Greenspan, whose support and vision set the ball in motion and made Mitotree possible.

Left to right, the Million Mito science team is:

  • Goran Runfeldt, Head of R&D at FamilyTreeDNA
  • Dr. Paul Maier, Senior Population Geneticist at FamilyTreeDNA
  • Roberta Estes, DNAexplain, scientist, blogger, author, genetic genealogist, and Genographic Affiliate Researcher
  • Dr. Miguel Vilar, Genetic Anthropologist, Lead Scientist with the Genographic Project, and Professor at the University of Maryland
  • Bennett Greenspan, President Emeritus of FamilyTreeDNA, and avid genealogist
  • John Detsikas, Front End Developer who is responsible for the user interface for both Y-DNA Discover and now mtDNA Discover

The Million Mito Project Inception

The Million Mito Project was launched at RootsTech 2020 and encouraged people to test their mitochondrial DNA, both for their genealogy and to help build the database. More than a million samples were candidates, but only high-quality, full sequence results were used. In the process of building the tree, additional samples were incorporated from other public sources for tree construction.

Drum Roll – The Mitotree

A beta version of the Mitotree is being released today, and boy, is this a big deal.

Before we discuss the rest of what’s coming, I need to mention that the Mitotree is now evergreen, meaning that the tree will be updated periodically, as will mtDNA Discover. This lifetime value is included with the cost of your test, so there’s nothing more to purchase.

Haplogroups will change from time to time, as the tree does, so don’t fall in love with yours, and definitely, no tattoos😊

I’m going to be speaking in terms of “we,” meaning the Million Mito team who built the Mitotree and mtDNA Discover, plus an amazing team of FamilyTreeDNA folks who were absolutely essential in getting this out the door and to you.

The Mitotree is new from the ground up, and yes, haplogroup naming consistency with PhyloTree has been maintained where possible.

One of the unanticipated challenges we encountered was that the 2016 PhyloTree had to be recreated, essentially reverse engineered, to determine the rules they used regarding mutations for haplogroup creation. In other words, which mutations were valid and reliable, which weren’t, determining their relative importance, and so forth.

After the existing 2016 tree was recreated, the next hurdle to overcome was that none of the existing phylogenetic software used in academia would scale from 24,000 samples and 5500 subclades to more than a quarter million samples and 40,000 haplogroups, so that software had to be designed and written by R&D team members.

More information about this process will be forthcoming shortly, and a paper will be published with our methodology, but for right now, let’s look at the user experience and what’s being released now.

Here’s what’s coming today and over the next few days.

The beta Mitotree includes:

  • Over 40,000 branches
  • Over 250,000 mtFull Sequences from FTDNA
  • Over 10,000 third-party full sequences from GenBank, 1000 Genomes, etc.
  • Over 1000 Ancient Connections
  • Over 100 Notable Connections

More is on the way.

The new Mitotree is the tree provided in several formats within mtDNA Discover. You can view the public version of the tree, here, or sign on to your FamilyTreeDNA account and click through from your dashboard to see more.

Today’s Releases

The Mitotree doesn’t exist in a vacuum, so several updates and new features will be rolling out today.

  • mtDNA Discover, which includes the new Mitotree
  • New customer haplogroups for those who have taken mtFull sequence tests
  • New mtDNA matches page

New Haplogroups

New haplogroups have been calculated for FamilyTreeDNA customers who have taken the full sequence test. Those who have taken only the HVR1 or HVR1/HVR2 tests are encouraged to upgrade to the full sequence test.

Not everyone will receive a new Mitotree haplogroup that is different from their classic haplogroup, but most people will. Your original haplogroup is displayed with the classic tag, and the new Mitotree haplogroup with the beta tag.

If your classic and Mitotree haplogroups are the same, it means that either you have no more private variants (mutations) available to form a new haplogroup, or no one else from your lineage has tested yet.

New mtDNA Matches Page

If you click on your mtDNA matches, you’ll notice that the page has been redesigned to look and function like the other FamilyTreeDNA match pages.

If you click to view your matches, you’ll be able to view both the “old” classic haplogroup, and your matches’ new Mitotree haplogroup, plus a new haplotype if they have one. We will talk about haplotypes in a minute.

The people you match are the same as before, but matches may be recalculated in the future.

If you click through to the new mtDNA Discover from your dashboard, you’ll be able to view the public portion of mtDNA Discover, plus the additional customized information provided to FamilyTreeDNA mtFull sequence customers.

mtDNA Discover

If you have taken a full sequence test, sign on to your account to view your new haplogroup, then click on the new mtDNA Discover icon on your dashboard.

If you haven’t taken the mtFull sequence test, but the partial HVR1 or HVR2 versions, you can still view mtDNA Discover on your dashboard, but without the mtFull customization.

Customization that occurs exclusively for FamilyTreeDNA mtFull sequence customers includes:

  • Most detailed placement of your branch on Mitotree
  • Haplotype clusters
  • Additional Ancient Connections
  • Additional Notable Connections
  • The Match Time Tree
  • Globetrekker (coming soon)
  • The Group Time Tree (coming soon)

mtDNA Discover is similar to Y-DNA Discover.

You’ll be able to view a dozen new reports about your haplogroup in addition to the tools provided on your dashboard.

The new Mitotree can be viewed in several formats, each with its unique benefit.

  1. Time Tree – a genetic tree that shows when each haplogroup was formed, plus a country flag for where present-day testers report as the location of their earliest known ancestor (EKA)
  2. Classic Tree – a more traditional view of a phylogenetic tree, including the number of testers on each branch, the variants, or mutations that define the haplogroup, the era and approximate date of formation, and other details about the tree topology
  3. Scientific Details Variants Tab – shows the variants that differ in each haplogroup as you reach back in time
  4. Ancestral Path for the selected haplogroup – outlines your path back to early humans, including Denisovans.
  5. Match Time Tree for you and your matches (must be signed in to your account and click on mtDNA Discover icon)
  6. Group Time Tree (coming soon) for those who have joined projects

Match Time Tree

The Match Time Tree is extremely useful because it overlays your matches, plus their earliest known ancestors (EKA), on a genetic Time Tree, by haplogroup and haplotype, so you can see how you may be related, and when.

You can also see your matches that have now fallen into neighboring haplogroups, which suggests that they probably aren’t as genealogically close as people in your haplogroup. However, that’s not always the case, because mutations can occur at any time.

Haplotype Clusters

A haplotype cluster is a new concept introduced specifically for genealogists with the new Mitotree. Haplotypes are identified by numbered “F” groups. Three are shown, below.

There may be groups of people within a haplogroup that have exactly the same mutations, or genetic signature, and no additional mutations. Still, they may not form a new haplogroup. There could be several reasons for not forming a new haplogroup, including known SNP locations where mutations occur that are known to be unstable, such as location  315, which tends to accumulate random insertions and is ignored because of its known instability.

When multiple people share an exactly identical signature, meaning all of the same mutations, they are shown within a haplotype “F” cluster to provide additional specificity to the tree.

The haplotype has been designed to provide additional granularity to the tree and genealogically relevant information. The haplotype “Fxxxxxx” numbers are randomly generated and have no special meaning.

A word of caution here. While the haplotype sequences are identical, it is still possible that another tester from outside the cluster could be a closer relative. For example, they could have accumulated a fast mutating SNP in the last few generations, which would give them a different signature.

Someone who is actually genealogically close to you may be in a different haplotype, or no haplotype at all because no one matches them exactly. For example, if your aunt or sister has a heteroplasmy, they are a close relative and will be in your haplogroup, but won’t be in your haplotype cluster because of the heteroplasmy. So don’t ignore matches who aren’t in your haplotype.

In the above example, under haplogroup V71b, there is one group of three people of unknown origin, meaning they didn’t enter any location for their earliest known ancestor, plus haplotype F9712482 – all of whom are identical matches to each other, but don’t form a new haplogroup.

Beneath V71b is haplogroup V71b1 with nine people, plus two haplotype clusters. F1965416 consists of two people, and F8189900 consists of 16 people.

You can also see haplotype clusters bracketed on any of the Time Trees in mtDNA Discover as well.

More to Come

There’s more information to come in the next few days and weeks, and at RootsTech. I’ll be writing articles when I get back.

For now, take a look to see if you have a new haplogroup. The new haplogroup rollout is being staggered, and you should receive an email when yours has been posted. But there’s no need to wait. Go ahead, sign in and check now, check out mtDNA Discover, and have fun.

Guaranteed, you’ll learn something new, and you may discover the key to a new ancestor!

Resources

Here are additional resources about the new Mitotree, mtDNA Discover, and the associated updates:

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Ancestry Updates Ethnicity, Renames Features, and Rearranges the Room

How many of you woke up recently to discover things were a bit different at Ancestry?

Ancestry has renamed their DNA tools, updated some of them, and essentially rearranged the furniture in the room.

It appears that the updates are rolling out to different users at different times, so if you don’t have these updates yet, you will soon.

A lot looks different and can be confusing until you figure out where things are.

Let’s start at the beginning – the first DNA option you see – the DNA Summary.

DNA Summary

Ancestry has rearranged the furniture with a new user interface and is in the process of updating some features, including ethnicity.

Your summary now looks like this.

New Terminology

Ancestry has changed their terminology too. No, I have no idea why.

What was previously called “Ethnicity” is now called “Ancestral Regions.”

What was previously called “Communities” is now called “Ancestral Journeys” and “Origins,” which is a very unfortunate choice because FamilyTreeDNA’s ethnicity feature is called myOrigins.

Nothing confusing here, right?

Where Are My Tests

Additionally, the location to find other DNA tests you have access to has changed as well. It’s not present on all pages, and it’s in a different location on some pages.

When in doubt or if you get lost, just go back to the main summary page.

On the main DNA Summary page, on the left, you’ll see your name with a down arrow. Click on the down arrow to display the names of others whose tests you have access to. In my case, I took the original Ancestry test and, later, the V2 test, which is why you see my name twice on the list, above, of DNA tests that I have access to.

Updated Regions

Ancestry has updated the regions and subregions that they report in their ethnicity, now “Ancestral Regions,” results.

Everyone is always excited to see their new results, but keep in mind that the smaller the size of reported regions becomes, the more like comparing ancestors from Indiana to ancestors from Illinois or Ohio and hoping to find enough genetic differences in order to separate them.

I wrote the article, Ethnicity is Just an Estimate – Yes, Really, a few years ago, and it’s just as true today as it was when I wrote it. That said, ethnicity is interesting and can be useful – just understand what you’re looking at and how it works.

The good news for genealogists is that updated ethnicity, at Ancestry or any other vendor, re-engages people and rekindles interest.

People not quite as interested in genealogy as we are might sign in to see “what’s new” and discover new matches or other interesting information. Genealogy, and genetic genealogy, are team sports so the more active players, the better. Whether you are happy or unhappy with your updated results, know that they serve as “bait” for the majority of testers.

Ancestral Regions

Ancestral Regions, previously known as ethnicity at Ancestry, are geographic locations where part of your DNA matches the DNA of people whose ancestors have, in theory, been there “forever.” People with known heritage in that region, and ostensibly no other regions, are called a “reference population,” and that group of people is who others, including you, are compared to.

Ancestry and other vendors tweak their results as new people and new populations are added. Sometimes, that tweaking improves things, and other times, not so much.

You’ll hear some people complaining loudly and others singing their praises with every update, regardless of which vendor.

My Native American DNA comes and goes at Ancestry. It’s back now.

This screenshot from February 2024 shows my V1 Ancestry test compared to my V2 test. One shows my Native heritage, and the other does not.

Unfortunately, without segment location information, there’s little more you can do with your ethnicity information unless there’s a high percentage of divergent regions. For example, European versus Native American versus African versus Asian. Continental differences are easy to discern from each other, and you can compare regions with your matches.

Another revelation might be a high percentage of a really surprising region that you weren’t expecting, which might suggest a grandparent or relatively close ancestor might have a different genealogy than you thought. Ireland versus Scotland isn’t surprising, given their location and migration heritage. However, Sweden versus Italy would be an unexpected finding if you thought you had a Swedish grandparent, for example, and instead you have 25% Italian.

Ancestral Journeys

In my own experience, Ancestral Journeys is much more useful than ethnicity (Ancestral Regions), but that isn’t universal, as we’ll see in a minute.

  1. Ancestral Journeys reflects where your ancestors lived within roughly 50-300 years, while Ancestral Regions (ethnicity) generally reaches back further in time.
  2. Ancestral Journeys regions are determined by common surnames of your DNA matches and where your matches’ ancestors lived, plus those same surnames and locations in your tree.

I find this information to be mostly accurate for my own tests, as far as it goes, but that’s not universal. Several regions are identified where my ancestors originated or lived in the US, but not in Europe, where 75% of my mother’s heritage was from prior to the 1880s.

Conversely, looking at the map, my mother had no Southern Louisiana French Settlers, but her Acadian cousins settled there, so that region makes perfect sense.

Divided By Parent

Ancestry encourages you to identify your ethnicity by parent, if possible, which allows them to divide (some of) your matches.

I wrote about how to accomplish this in the article, Ancestry’s SideView – Dividing Your Ethnicity in Two.

Alternatively, if you can’t identify which parent is which by ethnicity, if you can identify matches from either parental side, you can divide your matches that way as well.

This allows Ancestry to divide your results by parent, or at least try. They offer your Ancestral Regions (ethnicity), Ancestral Journeys (formerly Communities), and Chromosome Painter by parent.

Chromosome Painter

Ancestry paints your ethnicity regions on your chromosomes. You can view both your maternal and paternal chromosomes, or one at a time.

Ancestry’s Chromosome Painter shows an image, but doesn’t provide any additional useful information such as segment addresses.

In other words, I can see that Ancestry has assigned three separate segments of my DNA as Native American on my mother’s side, but they don’t provide that location so that I can compare it with other people to identify either a common segment that can be attributed to a specific ancestor, or common ethnicity.

However, you can upload your Ancestry DNA file to FamilyTreeDNA who provides chromosome painting PLUS ethnicity segment information, so you can determine which ancestor contributed that specific segment.

Additionally, DNAPainter allows you to paint your ethnicity and matching segments with others. Neither of those features is possible at Ancestry – so don’t get confused.

Origins By Parent

Ancestry divides, or attempts to divide, your Ancestral Regions (ethnicity) by parent.

In some cases, both parents may contribute DNA from some of the same world regions, as with mine, above. However, other regions are attributed to one parent and not the other.

Sometimes, you might notice that you have a small amount of DNA from a region that neither of your parents has. This is known as “noise” and happens when the DNA of your two parents combines in you to look like a different region. You can read more about how Ancestry does this division, here.

Journeys By Parent

You can view your Ancestral Journeys by parent as well.

My maternal journeys include the Acadian homeland in maritime Canada and another region that spans Pennsylvania, the Northern Blue Ridge, and on into Ohio.

Within that second orange grouping is a darker subgroup that includes Dayton, Ohio, shown with the green arrows, where Mom’s Brethren ancestors settled after migrating from Pennsylvania and Maryland.

Clicking on the region provides additional information, including a description and timeline of settlement in that region.

Ancestry connected the dots between this specific region and some ancestors shown in my tree, although these are just a few of my known ancestors who lived in Acadia.

Ancestry only shows a total of 7, but don’t limit your thinking to just what’s shown. I have more than 60 documented Acadian ancestors in my tree. In other words, don’t assume that Ancestry is showing you every ancestor you have that might fall into a region or category. Ancestry may be displaying only select ancestors.

Ancestry then shows selected matches by either Region or Journey.

Matches by Region and Journey

I need to say this in bright red before we review matches by Region and Journey, because it’s fundamentally important.

Just because you and another individual share a specific Ancestral Region or Ancestral Journey does NOT mean that your DNA and their DNA from that common Region or Journey is from a common ancestor that you share!

The DNA that you share may be from a completely different ancestor that lived in a region that neither of you show.

This is where genealogy research is required. Don’t be lulled into complacency and assume that because you share either a Region (ethnicity) or Journey (location settlement group) that your common ancestor is connected to either.

DNA Compare

That said, let’s take a look at these matching comparison features by scrolling all the way to the bottom and clicking on “DNA Compare.”

  • The first person shown is always you.
  • The second person is my other test at Ancestry.
  • The third person, Michael, is my first cousin, with whom I share 11% of my DNA and the same amount of Acadian heritage. We are both about 6.25% Acadian through our grandmother’s father’s paternal line.
  • Paul, a more distant cousin, and I share only our Acadian heritage.
  • This view shows both parents, so the fifth match is cousin Gregory, with whom I share known Danish ancestors. However, I have less than 1% Danish heritage, not the 16% that Ancestry has attributed. That’s a big difference and is unquestionably inaccurate.

Look at the results when we compare Ancestral Journeys for the same people I’m related to through my French Acadian heritage.

My two cousins who share Acadian DNA from Nova Scotia with me aren’t shown to be in the Canadian Maritimes Acadians Ancestral Journey. They clearly have numerous Acadian ancestors, and in Paul’s case, this is the only genealogical connection we share.

Michael and I share the same Acadian great-great-grandfather, Antoine Lore. Both of us would have inherited approximately 6.25% of his DNA, although not necessarily the same DNA. Antoine only had Acadian and Native American DNA to pass on to us, so any DNA descending from Antoine has to be one or the other.

Paul is 50% Acadian, and was assigned 49% French DNA, so he absolutely should have the Acadian Ancestral Journey. If you’re wondering if Michael and Paul are actually Acadian, they are, as proven by matches and shared matches.

While our Ancestral Regions both display some amount of “French,” neither Michael nor Paul are assigned the Acadian Journey. One might argue that Michael’s 5% French wasn’t sufficient to generate the Acadian Journey – but my 3% did – plus Michael and I share several Acadian matches and all of our Acadian ancestors.

Paul is another matter entirely. Regardless of our shared matches, with unquestionable 50% Acadian heritage, meaning his entire paternal line – there’s no reason Paul shouldn’t have been assigned an Acadian Journey.

So, what’s the moral of this story?

Don’t Get Too Attached

Don’t fall in love with ethnicity, now called Ancestral Origins, because it will change from time to time. So will your Ancestral Journeys.

For better or worse.

Maintain your genealogy skepticism and work to prove or disprove ethnicity and ethnicity-related information just as you would any other hint.

Evaluate your ethnicity percentages and locations based on known and proven genealogy. I wrote the article, Ancestral DNA Percentages – How Much of Them is in You?, where I explain how to determine, on average, what percent of each of your ancestors you would expect to inherit. Remember that recombination doesn’t give you that exact percentage, though. You could have inherited more or less.

Evaluate Ancestral Origins, Ancestral Journeys, and other relationship information, such as shared matches, logically. Does anything conflict? Does anything not make sense? Did anything click? Was there an “aha” moment?

Are there surprises that you wouldn’t have expected, and can you identify other forms of corroborating evidence? Build a case, and be sure to include genealogical information in the mix as well.

Essentially, treat everything as a hint to be proven or disproven.

Furthermore, be gentle with yourself as you learn your way around the rearranged furniture in the room. You might trip over the coffee table, but you can’t break it, so scroll around and click on everything to gather as much information as possible.

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Thank you so much.

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